Variant report

Variant	rs2488389
Chromosome Location	chr1:197631141-197631142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197628715..197631555-chr1:197637374..197639292,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10737693	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11583319	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11588864	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11799915	0.98[ASN][1000 genomes]
rs12092948	0.96[ASN][1000 genomes]
rs12117045	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12131588	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12141028	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12354257	1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[ASN][1000 genomes]
rs12724239	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12748009	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1421399	0.93[ASN][1000 genomes]
rs1539414	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs1573100	0.93[ASN][1000 genomes]
rs16841842	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841904	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16841912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17564924	0.98[ASN][1000 genomes]
rs17621130	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17641524	1.00[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs1775448	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1775452	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1998598	0.87[ASN][1000 genomes]
rs2224873	0.93[EUR][1000 genomes]
rs2477059	0.93[ASN][1000 genomes]
rs2477073	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2477077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2488391	0.84[ASN][1000 genomes]
rs2488393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2488397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2488398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2488401	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2884629	0.92[ASN][1000 genomes]
rs35939830	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4316387	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6682968	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6702421	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv548872	chr1:197529218-197644581	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv873076	chr1:197529218-197689967	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	esv3397065	chr1:197545083-197637033	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv437263	chr1:197599030-197722240	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv427908	chr1:197611569-197767362	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv873077	chr1:197615391-197698103	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Inflammatory bowel disease	23128233	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2488389	DENND1B	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197596600-197644800	Weak transcription	Ovary	ovary
2	chr1:197602800-197641400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr1:197603000-197632400	Weak transcription	Fetal Lung	lung
4	chr1:197603000-197632600	Weak transcription	Small Intestine	intestine
5	chr1:197603200-197645000	Weak transcription	Esophagus	oesophagus
6	chr1:197603400-197643400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:197604200-197635200	Weak transcription	Aorta	Aorta
8	chr1:197608600-197631400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:197610200-197640000	Weak transcription	Fetal Intestine Small	intestine
10	chr1:197611800-197644800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:197612200-197642200	Weak transcription	Primary B cells from cord blood	blood
12	chr1:197612800-197644800	Weak transcription	Fetal Intestine Large	intestine
13	chr1:197612800-197645000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:197619800-197633600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:197627200-197632600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:197627400-197637600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:197628800-197632600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:197628800-197645000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:197629000-197632400	Weak transcription	Liver	Liver
20	chr1:197629000-197633600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr1:197629000-197640400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:197629000-197644600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:197629000-197645000	Weak transcription	Dnd41	blood
24	chr1:197629000-197645200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:197630200-197632000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:197630200-197632400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:197630200-197633600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr1:197630800-197631200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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